The Scottish Senior Football Referees Association has this week criticised the "lenient" punishment handed out to Nadir Ciftci for manhandling a linesman.
The Dundee United forward was given a two-match ban, one of which is suspended, for "placing an open hand into the lower area of the assistant referee's throat".
Speaking on Thursday, Celtic boss Neil Lennon agreed that match officials should be protected but felt they should also explain their decisions if they want to have a say on cases such as the Ciftci ban.
Asked about the issue, McCoist said: "I think they should have protection whether they come out and say anything after games or not.
"Referees should be absolutely guaranteed protection to be honest with you.
"I think the referees do a fantastic job under increasingly difficult circumstances. I certainly would not start publicly criticising referees, no way."
He added: "I don't think they want it both ways. Obviously, in an ideal world, we would like to hear from referees and understand why they made a decision.
"Referees will make mistakes just like the rest of us. Players will make mistakes and managers make more mistakes than most.
"I can understand it would be nice to hear possibly why they made a mistake, the same way we probably have to make explanations for our mistakes.
"But I've got the greatest of sympathy for referees."
The Scottish Football Association was unhappy with the referees' union for making a public statement, with the group standing by their criticism of the punishment.
McCoist said: "I can totally understand their frustration and they are well within their rights to argue their case, which I don't have any doubts they will do.
"They should be protected, particularly on a football park.
"In modern times, with modern technology, refereeing and being a linesman is increasingly difficult, with the speed of the game and television cameras.
"I think they do a very good job under increasingly difficult circumstances."
Meanwhile, McCoist says he has not been given assurances that the club will not sell players when the transfer window opens next month.
He said: "No, I haven't received any assurances like that at all. But, to be fair, I haven't been looking for them.
"If and when something like that happens, no doubt we will be talking."
And McCoist has not had any detailed discussions about possible reinforcements in January either.
Speaking ahead of Saturday's visit of Ayr United in Scottish League One, he said: "I haven't had a good chance to sit down and discuss it yet.
"We are pleased with the way things are going at the moment.
"It's our job, at this particular time in the club's history, to continue to look forward and plan for the future.
"We will continue to do that and see what happens in the next couple of weeks or so."